Contacts of the helix formed by residues 269 - 284 (chain A) in PDB entry 3P9K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A TRP* 1.3 78.6 - - - +
270A ASP* 1.3 64.3 + - - +
271A GLN* 3.5 7.8 + - - +
272A HIS* 2.9 30.9 + - - +
273A CYS* 3.0 20.4 + - - -
322A PRO 3.2 14.2 + - - -
323A GLY* 3.5 17.9 - - - -
325A ARG* 5.5 1.1 - - - +
327A ARG* 3.5 1.3 - - - +
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A SER* 1.3 73.3 - - - +
271A GLN* 1.3 59.2 + - - +
273A CYS* 3.2 3.0 + - - +
274A ALA* 2.8 30.0 + - - +
325A ARG* 4.4 9.4 + - - +
327A ARG* 2.9 31.2 + - - +
331A GLU* 6.1 0.2 - - - +
335A LEU* 4.0 19.8 - - + +
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A SER* 3.2 8.8 + - - +
270A ASP* 1.3 78.5 - - - +
272A HIS* 1.3 68.7 + - + +
274A ALA* 3.1 13.0 + - - +
275A THR* 3.0 33.4 + - - +
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Residues in contact with HIS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PHE* 3.4 28.6 - + + -
268A TRP* 3.4 51.7 - + + -
269A SER* 2.9 24.3 + - - +
271A GLN* 1.3 82.8 - - + +
273A CYS* 1.3 52.4 + - - +
275A THR* 3.1 8.9 + - - -
276A LEU 2.8 29.6 + - - -
322A PRO* 4.8 9.5 - - + +
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Residues in contact with CYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 3.5 49.8 - - + -
268A TRP* 3.6 10.8 - - - -
269A SER 3.0 18.6 + - - -
270A ASP 3.6 7.2 - - - +
272A HIS* 1.3 73.6 - - - +
274A ALA* 1.3 58.8 + - - +
276A LEU* 4.2 7.4 - - - -
277A LEU* 2.6 41.7 + - + +
327A ARG* 3.7 10.1 - - - -
335A LEU* 4.2 17.3 - - + -
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASP 2.8 14.7 + - - +
271A GLN* 3.1 23.3 + - - +
273A CYS* 1.3 76.3 - - - +
275A THR* 1.3 62.1 + - - +
277A LEU* 4.0 4.1 - - - +
278A LYS* 3.1 25.3 + - - +
335A LEU* 4.7 9.4 - - + +
339A ALA* 5.0 3.4 - - - +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PHE* 3.7 33.4 - - + +
271A GLN* 3.0 26.1 + - - +
272A HIS* 3.4 10.2 - - - -
274A ALA* 1.3 78.0 - - - +
276A LEU* 1.3 63.2 + - - +
278A LYS* 3.3 5.3 + - - +
279A ASN* 3.2 25.7 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 4.2 5.8 - - + -
249A MET* 3.6 48.5 - - + +
250A PHE* 4.1 11.2 - - + -
253A VAL* 4.3 2.9 - - + -
261A MET* 3.7 26.2 - - + -
264A ILE* 3.8 20.9 - - + -
265A LEU* 3.9 11.4 - - + -
268A TRP* 5.3 2.2 - - + -
272A HIS 2.8 19.4 + - - +
273A CYS* 3.7 5.4 - - - +
275A THR* 1.3 72.9 - - - +
277A LEU* 1.3 62.7 + - - +
279A ASN* 3.0 11.3 + - - +
280A CYS* 3.0 30.0 + - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A MET* 3.7 28.9 - - + -
265A LEU* 4.3 16.2 - - + -
273A CYS 2.6 24.6 + - - +
274A ALA* 4.2 2.5 - - - +
276A LEU* 1.3 73.8 - - - +
278A LYS* 1.3 55.6 + - - +
280A CYS* 3.4 4.1 + - - +
281A TYR* 3.0 28.4 + - - +
290A VAL* 4.6 6.5 - - + -
335A LEU* 3.7 39.0 - - + +
336A ALA* 4.7 0.4 - - - -
339A ALA* 3.7 15.3 - - + -
341A PHE* 3.8 9.7 - - + -
358A PHE* 3.8 30.7 - - + -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ALA 3.1 19.3 + - - +
275A THR* 3.5 6.1 - - - +
277A LEU* 1.3 73.1 - - - +
279A ASN* 1.3 75.2 + - - +
281A TYR* 3.2 7.6 + - + +
282A ASP* 3.0 59.7 + - - +
339A ALA* 4.1 15.0 - - + +
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Residues in contact with ASN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A MET 3.1 20.5 + - - +
250A PHE* 2.9 31.1 + - - +
251A LYS 3.7 8.1 + - - +
252A GLU* 4.3 14.1 - - - -
253A VAL* 3.8 7.9 + - + +
275A THR* 3.2 16.9 + - - +
276A LEU 3.0 7.9 + - - +
278A LYS* 1.3 87.5 + - - +
280A CYS* 1.3 63.1 + - - +
282A ASP* 3.5 8.7 + - - +
283A ALA* 3.1 23.4 + - - +
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 4.7 1.3 - - - -
253A VAL* 4.0 6.7 - - - -
259A ILE* 3.8 30.7 - - + -
261A MET* 3.9 33.7 - - - -
276A LEU* 3.0 26.2 + - - -
277A LEU* 3.6 8.5 - - - +
279A ASN* 1.3 74.5 - - - +
281A TYR* 1.3 67.1 + - - +
283A ALA* 2.9 14.2 + - - +
284A LEU* 3.2 18.1 + - - +
290A VAL* 3.8 15.0 - - + -
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LEU 3.0 14.1 + - - +
278A LYS* 3.3 9.9 - - + +
280A CYS* 1.3 77.8 - - - +
282A ASP* 1.3 75.7 + - - +
284A LEU* 3.4 2.4 + - - -
339A ALA 3.6 19.3 - - - +
340A GLY* 3.6 28.8 + - - -
341A PHE* 3.7 27.3 - + + -
360A LYS* 2.9 71.0 + - + +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LYS* 3.0 51.9 + - - +
279A ASN* 3.9 7.6 - - - +
280A CYS 3.1 0.2 - - - -
281A TYR* 1.3 88.7 - - - +
283A ALA* 1.3 57.7 + - - +
284A LEU 3.0 15.9 + - - +
360A LYS* 5.2 0.4 - - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A VAL* 3.5 30.1 - - + +
254A PRO 3.6 12.1 - - - +
255A SER* 3.3 25.9 + - - +
256A GLY 3.3 11.8 + - - +
259A ILE* 4.4 2.7 - - + -
279A ASN 3.1 15.3 + - - +
280A CYS 2.9 6.2 + - - +
282A ASP* 1.3 75.3 - - - +
284A LEU* 1.3 60.2 + - - +
285A PRO* 4.5 0.2 - - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A GLY 3.3 18.6 - - - +
257A ASP 3.9 19.3 - - - +
258A THR 3.9 0.4 - - - +
259A ILE* 3.7 24.2 - - + -
280A CYS 3.2 14.3 + - - +
281A TYR* 3.6 8.9 - - - +
282A ASP 3.0 8.1 - - - +
283A ALA* 1.3 81.3 - - - +
285A PRO* 1.3 66.3 - - + +
288A GLY* 4.1 3.1 - - - -
289A LYS* 3.6 33.4 - - - +
290A VAL* 3.8 16.8 - - + +
341A PHE* 4.3 11.2 - - + -
360A LYS* 2.8 21.9 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il